LAMMPS (27 Nov 2018)
  using 1 OpenMP thread(s) per MPI task
# 2d circle of particles inside a box with LJ walls

variable        b index 0

variable	x index 50
variable	y index 20
variable	d index 20
variable	v index 5
variable	w index 2

units		lj
dimension       2
atom_style	bond
boundary        f f p

lattice		hex 0.85
Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
region		box block 0 $x 0 $y -0.5 0.5
region		box block 0 50 0 $y -0.5 0.5
region		box block 0 50 0 20 -0.5 0.5
create_box	1 box bond/types 1 extra/bond/per/atom 6
Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
  2 by 2 by 1 MPI processor grid
region		circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region		circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region		circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
region		circle sphere 11 6.7735026918962581988 0.0 10
create_atoms	1 region circle
Created 361 atoms
  Time spent = 0.00067687 secs
mass		1 1.0

velocity	all create 0.5 87287 loop geom
velocity        all set $v $w 0 sum yes
velocity        all set 5 $w 0 sum yes
velocity        all set 5 2 0 sum yes

pair_style	lj/cut 2.5
pair_coeff	1 1 10.0 1.0 2.5

bond_style      harmonic
bond_coeff      1 10.0 1.2

# need to preserve 1-3, 1-4 pairwise interactions during hard collisions

special_bonds   lj/coul 0 1 1
  0 = max # of 1-2 neighbors
  1 = max # of special neighbors
create_bonds    many all all 1 1.0 1.5
Neighbor list info ...
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 2.8
  binsize = 1.4, bins = 42 29 1
  2 neighbor lists, perpetual/occasional/extra = 1 1 0
  (1) command create_bonds, occasional
      attributes: full, newton on
      pair build: full/bin
      stencil: full/bin/2d
      bin: standard
  (2) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/2d/newton
      bin: standard
Added 1014 bonds, new total = 1014
  6 = max # of 1-2 neighbors
  6 = max # of special neighbors

neighbor	0.3 bin
neigh_modify	delay 0 every 1 check yes

fix		1 all nve

fix             2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
fix             2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
fix             3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
fix             3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5

comm_style      tiled
comm_modify     cutoff 10.0   # because bonds stretch a long ways
fix             10 all balance 50 0.9 rcb

#compute         1 all property/atom proc
#variable        p atom (c_1%10)+1
#dump            2 all custom 50 tmp.dump id v_p x y z

#dump            3 all image 50 image.*.jpg v_p type bond atom 0.25 #                adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
#variable        colors string #                "red green blue yellow white #                purple pink orange lime gray"
#dump_modify     3 pad 5 amap 0 10 sa 1 10 ${colors}

thermo_style    custom step temp epair press f_10[3] f_10
thermo          100

run		10000
Neighbor list info ...
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 10
  binsize = 1.4, bins = 42 29 1
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/2d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.122 | 5.141 | 5.174 Mbytes
Step Temp E_pair Press f_10[3] f_10 
       0    25.701528   -2.2032569    3.1039469    3.2354571    1.0526316 
     100    27.623422    -6.228166    2.6542136    1.2631579    1.0083102 
     200     33.35302   -15.746749    3.2018248    1.2963989    1.0193906 
     300     39.17734     -24.1557    4.9116986    1.2963989    1.0193906 
     400    41.660701   -27.615203    8.6214679    1.3518006    1.0083102 
     500    37.154928   -24.096946    3.2656177    1.3296399    1.0304709 
     600    35.059873   -21.524223    2.3729526    1.3296399    1.0083102 
     700    36.735117   -22.012675     3.266197    1.3296399    1.0083102 
     800    39.218223   -25.076176    4.7162461    1.4182825    1.0193906 
     900    38.003628   -24.598176    3.4651756    1.4958449    1.0083102 
    1000    37.599298   -25.117714    4.6714491    1.2963989    1.0193906 
    1100    35.587211   -24.476201    4.8766816    1.2077562    1.0083102 
    1200     33.05745   -21.457847    4.7304313    1.2188366    1.0193906 
    1300    35.505899   -20.103017    7.0543469    1.1523546    1.0193906 
    1400    32.687958   -18.411286    2.8022421    1.1523546    1.0083102 
    1500    30.681103   -13.979491    1.5780815    1.1523546    1.0083102 
    1600    28.134276   -12.408217    1.4370834    1.2188366    1.0193906 
    1700    29.150676   -12.486223    1.7118526    1.1745152    1.0083102 
    1800    29.456937   -11.386522    2.0484739    1.1966759    1.0193906 
    1900    28.029998   -11.168436   0.38519481    1.1080332    1.0193906 
    2000    29.476997   -12.337678    1.8878345    1.1523546    1.0083102 
    2100    30.113294   -12.201714    2.8003366    1.1634349    1.0193906 
    2200    31.599067   -13.710787    2.5654923    1.2188366    1.0083102 
    2300    31.333799   -12.269386    1.9573739    1.1412742    1.0193906 
    2400    28.587094    -10.98229     2.090581    1.1745152    1.0083102 
    2500    28.012332   -11.416553    2.3293146    1.1855956    1.0083102 
    2600    28.703189    -13.33369    2.7247345    1.1080332    1.0083102 
    2700    26.933934   -13.546384   0.71447362    1.0415512    1.0304709 
    2800    24.556936   -12.231427  0.012081842    1.0526316    1.0193906 
    2900    24.362943   -10.921093   -0.6063159    1.0858726    1.0193906 
    3000    24.583358   -10.025143   0.35975315    1.0637119    1.0083102 
    3100    26.119046   -10.124317   0.75140102    1.0415512    1.0193906 
    3200    27.665317   -11.418452   0.39942176    1.1301939    1.0083102 
    3300    27.771434   -9.9777413   0.94693011    1.1080332    1.0083102 
    3400    25.692188   -9.9016885    2.2582772    1.0415512    1.0083102 
    3500    27.009276   -10.504438   0.98279258    1.1301939    1.0083102 
    3600    26.082843   -9.4359595 -0.030819747    1.1301939    1.0083102 
    3700    23.956851   -8.4601884  -0.45748969    1.0858726    1.0304709 
    3800     24.92141   -8.3315871  -0.19512647    1.0969529    1.0083102 
    3900    26.048044   -9.6299934   0.40522014    1.0858726    1.0083102 
    4000    26.558961   -10.032084   0.56213613    1.1745152    1.0083102 
    4100    26.949686   -10.133598    1.0140825    1.0747922    1.0083102 
    4200    25.868196   -9.3971859    1.2758465    1.0969529    1.0083102 
    4300    24.563369   -9.5992996   0.17389949    1.1191136    1.0193906 
    4400    24.032818   -10.002668   0.10233743    1.0969529    1.0083102 
    4500    25.281577    -9.948799    0.7590423    1.1523546    1.0083102 
    4600    25.010901   -10.195479  -0.24424931    1.0747922    1.0193906 
    4700    25.062368   -9.2973021    1.1755931    1.0858726    1.0193906 
    4800     25.70912    -8.890895    1.0780397    1.1080332    1.0193906 
    4900    26.027757   -10.205469    1.0644859    1.1080332    1.0083102 
    5000    25.845739   -9.8511049   0.49059257    1.1301939    1.0193906 
    5100    25.614064   -9.0396911   0.40825814    1.0526316    1.0304709 
    5200    25.548135    -9.000613   0.81571441    1.1080332    1.0083102 
    5300    26.592601   -9.2385129    1.4983434    1.0637119    1.0193906 
    5400    26.230779   -9.8226036    1.0072462    1.0858726    1.0083102 
    5500    26.809887   -9.9569954    1.4074968    1.0415512    1.0083102 
    5600    25.722206   -10.240487   -0.5216434    1.0747922    1.0193906 
    5700    24.973866   -9.0820997   0.92104357    1.0193906    1.0083102 
    5800    24.257134   -9.5439897  -0.75290789    1.0858726    1.0083102 
    5900    25.524917   -8.9920216    1.2049479    1.1191136    1.0083102 
    6000    24.816532   -9.5865764  -0.66634446    1.0637119    1.0193906 
    6100    27.034385   -9.4017037    1.0769494    1.0969529    1.0083102 
    6200     24.19144   -8.2292864   0.97913204    1.0415512    1.0193906 
    6300    26.112877   -9.1531212   0.77578963    1.0526316    1.0193906 
    6400    25.820541   -9.9662231 -0.092724413    1.0969529    1.0193906 
    6500    26.181404   -9.5875764  -0.30106405    1.1634349    1.0083102 
    6600    27.770851   -8.8366116   0.94545206    1.0304709    1.0193906 
    6700    26.065489   -9.8223382   0.24640067    1.0526316    1.0193906 
    6800    27.468165   -10.160923    2.7263738    1.0747922    1.0304709 
    6900    27.317955   -10.356911     1.131609    1.0526316    1.0304709 
    7000    26.343789   -9.9153453    1.0385354    1.0858726    1.0193906 
    7100    24.366577   -8.9243936   0.37685043    1.0526316    1.0193906 
    7200    25.570042   -8.9195237   0.44206575    1.0637119    1.0193906 
    7300    24.635046   -8.4524117  -0.20581694    1.0193906    1.0193906 
    7400    27.161863   -7.9885934    1.1323072    1.0858726    1.0193906 
    7500      26.8044   -9.5703931   0.69476535    1.0858726    1.0193906 
    7600    27.381006   -10.702178  -0.20230101    1.0526316    1.0083102 
    7700    26.507406    -9.828117   0.50115907    1.0415512    1.0193906 
    7800    25.945271   -8.9912842   0.89121191    1.0747922    1.0083102 
    7900    24.498681   -7.7193231  -0.63874494    1.0858726    1.0083102 
    8000    24.517408   -7.6046107  -0.91642337    1.0415512    1.0083102 
    8100    26.388387   -8.1883906  0.093136981    1.1080332    1.0193906 
    8200    26.261054   -8.7223732 -0.086859057    1.0747922    1.0083102 
    8300    26.287026   -9.2583895   0.79506804    1.0858726    1.0083102 
    8400    24.691375   -9.0701909  -0.40058151    1.0637119    1.0193906 
    8500    25.390612   -7.9499801   0.59874113    1.1412742    1.0193906 
    8600     26.84383   -8.5520984   0.37618599    1.0637119    1.0083102 
    8700    25.685137    -7.688836  0.035978149    1.0415512    1.0193906 
    8800    26.614591   -9.0444146   0.20671465    1.0193906    1.0083102 
    8900    25.782718   -8.2594705   0.54378816    1.0747922    1.0304709 
    9000    26.026886   -8.6777252   0.25418163    1.1191136    1.0083102 
    9100    27.246916   -9.0307861     1.211131    1.0526316    1.0193906 
    9200    27.282948    -9.180029 -0.0056269613    1.0747922    1.0083102 
    9300    27.029692   -8.7791461   0.35971649    1.0304709    1.0083102 
    9400    26.549013   -7.5083174   0.77607249    1.0969529    1.0193906 
    9500    25.533731   -9.2763668   0.28360762    1.0969529    1.0083102 
    9600    27.997538   -9.2766769    1.6968428    1.0637119    1.0083102 
    9700    26.977436     -9.21372    1.8007256    1.0637119    1.0083102 
    9800    25.547091   -9.1024445  -0.29158273    1.0969529    1.0193906 
    9900    26.378841   -8.7645665    1.0385835    1.1080332    1.0083102 
   10000    26.699368   -8.5450739   0.19591452    1.0526316    1.0193906 
Loop time of 0.916576 on 4 procs for 10000 steps with 361 atoms

Performance: 4713193.307 tau/day, 10910.170 timesteps/s
92.2% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.10915    | 0.12374    | 0.14167    |   3.5 | 13.50
Bond    | 0.047075   | 0.049849   | 0.054161   |   1.2 |  5.44
Neigh   | 0.31176    | 0.3246     | 0.3384     |   1.7 | 35.41
Comm    | 0.24271    | 0.26717    | 0.30549    |   4.9 | 29.15
Output  | 0.0017068  | 0.0021075  | 0.0031145  |   1.3 |  0.23
Modify  | 0.064639   | 0.065705   | 0.067641   |   0.5 |  7.17
Other   |            | 0.08341    |            |       |  9.10

Nlocal:    90.25 ave 92 max 89 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost:    248.25 ave 264 max 230 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs:    569.5 ave 657 max 519 min
Histogram: 2 0 0 0 1 0 0 0 0 1

Total # of neighbors = 2278
Ave neighs/atom = 6.31025
Ave special neighs/atom = 5.61773
Neighbor list builds = 4964
Dangerous builds = 14
Total wall time: 0:00:00
